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Chlorine in PDB 3ka4: Frog M-Ferritin with Cobalt

Enzymatic activity of Frog M-Ferritin with Cobalt

All present enzymatic activity of Frog M-Ferritin with Cobalt:
1.16.3.1;

Protein crystallography data

The structure of Frog M-Ferritin with Cobalt, PDB code: 3ka4 was solved by T.Tosha, H.L.Ng, E.Theil, T.Alber, O.Bhattasali, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.40
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.765, 183.765, 183.765, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 17.4

Other elements in 3ka4:

The structure of Frog M-Ferritin with Cobalt also contains other interesting chemical elements:

Cobalt (Co) 8 atoms
Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Frog M-Ferritin with Cobalt (pdb code 3ka4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Frog M-Ferritin with Cobalt, PDB code: 3ka4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3ka4

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Chlorine binding site 1 out of 8 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl184

b:32.9
occ:1.00
 NE2 A:HIS61 3.1 20.4 1.0
O A:HOH366 3.6 24.0 1.0
CD2 A:HIS61 3.7 18.3 1.0
O A:HOH419 3.7 39.2 1.0
CG A:GLU57 4.1 20.7 0.5
OE1 A:GLU136 4.1 32.7 1.0
CD A:GLU136 4.2 29.8 1.0
CG A:GLU136 4.3 24.2 1.0
CE1 A:HIS61 4.3 21.9 1.0
OE2 A:GLU136 4.6 26.9 1.0
OE1 A:GLU57 4.7 27.0 0.5
CB A:GLU136 4.8 17.9 1.0
CB A:GLU57 4.8 15.6 0.5
CG A:HIS61 4.9 18.0 1.0

Chlorine binding site 2 out of 8 in 3ka4

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Chlorine binding site 2 out of 8 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl189

b:26.4
occ:1.00
 OG1 A:THR105 3.2 13.4 1.0
O A:HOH256 3.2 18.1 1.0
CA A:LEU102 3.6 11.2 1.0
O A:GLN101 3.7 13.6 1.0
O A:HOH259 3.7 32.5 1.0
CG A:GLN101 3.7 16.4 0.5
N A:LEU102 3.7 11.3 1.0
C A:GLN101 3.8 12.3 1.0
CB A:THR105 3.8 11.0 1.0
NE2 A:GLN101 4.0 25.6 0.5
CD A:GLN101 4.2 21.5 0.5
CB A:GLN101 4.2 14.2 0.5
CB A:LEU102 4.3 11.9 1.0
CD1 A:LEU102 4.3 15.7 1.0
CG2 A:THR105 4.4 13.3 1.0
CB A:GLN101 4.4 13.8 0.5
CA A:GLN101 4.7 12.7 0.5
CA A:GLN101 4.7 12.5 0.5
O A:HOH278 4.8 23.1 1.0
C A:LEU102 4.8 10.6 1.0
O A:HOH384 4.8 23.5 1.0
O A:LEU102 5.0 11.5 1.0
CG A:LEU102 5.0 13.3 1.0

Chlorine binding site 3 out of 8 in 3ka4

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Chlorine binding site 3 out of 8 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl190

b:24.0
occ:1.00
 N A:ASP87 3.2 13.2 1.0
N A:GLU88 3.7 12.1 1.0
CA A:ARG86 3.8 12.8 1.0
CB A:ARG86 3.8 13.8 1.0
C A:ARG86 4.0 12.6 1.0
CA A:ASP87 4.0 13.0 1.0
O A:GLU88 4.0 13.6 1.0
CG A:GLU88 4.0 13.4 0.5
CB A:ASP87 4.0 14.1 1.0
CG A:ARG86 4.3 16.7 1.0
C A:ASP87 4.3 13.2 1.0
CB A:GLU88 4.4 14.2 0.5
CA A:GLU88 4.5 12.9 0.5
NE A:ARG86 4.6 22.6 1.0
CA A:GLU88 4.6 12.2 0.5
OE2 A:GLU88 4.6 23.2 0.5
CG A:ASP87 4.7 16.4 1.0
OD2 A:ASP87 4.7 22.7 1.0
C A:GLU88 4.7 11.9 1.0
CB A:GLU88 4.7 13.2 0.5

Chlorine binding site 4 out of 8 in 3ka4

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Chlorine binding site 4 out of 8 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl191

b:24.8
occ:1.00
 NZ A:LYS82 2.8 24.8 0.0
NZ A:LYS82 3.2 26.7 1.0
CE A:LYS82 3.3 18.5 0.0
CE A:LYS82 3.3 18.9 1.0
O A:HOH368 4.8 28.9 1.0
CD A:LYS82 4.8 16.6 0.0
CD A:LYS82 4.8 15.8 1.0

Chlorine binding site 5 out of 8 in 3ka4

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Chlorine binding site 5 out of 8 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl192

b:20.3
occ:1.00
 N A:TYR8 3.3 11.5 1.0
O A:HOH370 3.3 32.5 1.0
N A:ASN7 3.4 11.9 1.0
O A:TYR8 3.5 13.9 1.0
CG A:ARG5 3.5 14.7 1.0
CD A:ARG5 3.6 16.7 1.0
NE A:ARG5 3.6 14.4 1.0
O A:HOH279 3.8 21.7 1.0
C A:GLN6 3.9 10.9 1.0
CA A:GLN6 4.0 10.6 1.0
C A:TYR8 4.0 11.2 1.0
N A:GLN6 4.0 11.4 1.0
CA A:TYR8 4.1 11.1 1.0
CA A:ASN7 4.1 11.4 1.0
C A:ASN7 4.2 11.4 1.0
C A:ARG5 4.3 12.3 1.0
CB A:ARG5 4.4 12.9 1.0
CB A:TYR8 4.4 11.4 1.0
O A:ARG5 4.5 12.7 1.0
O A:GLN6 4.8 11.3 1.0
CZ A:ARG5 4.9 12.9 1.0
CA A:ARG5 5.0 12.1 1.0

Chlorine binding site 6 out of 8 in 3ka4

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Chlorine binding site 6 out of 8 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl193

b:29.3
occ:1.00
 N A:SER10 3.1 11.8 1.0
CB A:SER10 3.7 13.6 1.0
CA A:HIS9 3.8 12.5 1.0
O A:HOH370 3.8 32.5 1.0
CD2 A:HIS9 3.8 16.1 1.0
CG A:HIS9 3.9 14.5 1.0
C A:HIS9 4.0 11.2 1.0
NE2 A:HIS9 4.0 19.3 1.0
CA A:SER10 4.0 12.4 1.0
ND1 A:HIS9 4.0 16.3 1.0
CE1 A:HIS9 4.1 12.6 1.0
O A:TYR8 4.4 13.9 1.0
CB A:HIS9 4.4 12.5 1.0
O A:HOH239 4.5 37.7 1.0
N A:HIS9 4.9 12.1 1.0

Chlorine binding site 7 out of 8 in 3ka4

Go back to Chlorine Binding Sites List in 3ka4
Chlorine binding site 7 out of 8 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl194

b:20.3
occ:1.00
 O A:HOH414 3.1 32.6 1.0
N A:GLU136 3.2 14.3 1.0
O A:HOH338 3.2 19.9 1.0
C A:GLU132 3.4 12.0 1.0
N A:TYR133 3.4 11.1 1.0
N A:GLU135 3.4 11.9 1.0
C A:TYR133 3.7 11.7 1.0
O A:GLU132 3.7 15.1 1.0
O A:SER131 3.7 15.3 1.0
CB A:GLU135 3.7 14.8 1.0
CA A:GLU135 3.8 12.5 1.0
CA A:TYR133 3.9 11.5 1.0
CA A:GLU132 3.9 12.5 1.0
N A:LEU134 3.9 11.6 1.0
O A:HOH367 3.9 33.5 1.0
C A:GLU135 3.9 13.8 1.0
C A:SER131 3.9 13.6 1.0
CB A:GLU136 4.0 17.9 1.0
N A:GLU132 4.0 13.0 1.0
O A:TYR133 4.0 13.4 1.0
CA A:GLU136 4.2 14.5 1.0
O A:GLU130 4.2 14.9 1.0
C A:LEU134 4.4 11.5 1.0
CG A:GLU135 4.4 15.0 1.0
O A:HOH332 4.6 22.6 1.0
CA A:LEU134 4.8 11.2 1.0
O A:HOH339 4.9 19.0 1.0
CA A:SER131 4.9 13.8 1.0
MG A:MG197 5.0 30.0 1.0

Chlorine binding site 8 out of 8 in 3ka4

Go back to Chlorine Binding Sites List in 3ka4
Chlorine binding site 8 out of 8 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl195

b:14.9
occ:0.25
 CO A:CO179 2.3 13.0 0.2
NE2 A:HIS169 3.2 12.1 1.0
CE1 A:HIS169 3.3 13.3 1.0
CD2 A:LEU165 3.6 13.9 1.0
CD2 A:HIS169 4.4 12.8 1.0
ND1 A:HIS169 4.5 12.8 1.0
O A:HOH345 4.7 14.6 0.2
CG A:LEU165 5.0 13.1 1.0

Reference:

T.Tosha, H.L.Ng, O.Bhattasali, T.Alber, E.C.Theil. Moving Metal Ions Through Ferritin-Protein Nanocages From Three-Fold Pores to Catalytic Sites. J.Am.Chem.Soc. V. 132 14562 2010.
ISSN: ISSN 0002-7863
PubMed: 20866049
DOI: 10.1021/JA105583D
Page generated: Sat Jul 20 22:30:41 2024

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